US9580749B2 - Dyes and labeled molecules - Google Patents
Dyes and labeled molecules Download PDFInfo
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- US9580749B2 US9580749B2 US13/968,122 US201313968122A US9580749B2 US 9580749 B2 US9580749 B2 US 9580749B2 US 201313968122 A US201313968122 A US 201313968122A US 9580749 B2 US9580749 B2 US 9580749B2
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- dye
- nucleic acid
- fluorescent
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- independently
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- C07D209/04—Indoles; Hydrogenated indoles
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- C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
- C07D213/24—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with substituted hydrocarbon radicals attached to ring carbon atoms
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- C07D491/12—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains three hetero rings
- C07D491/14—Ortho-condensed systems
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- C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
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Abstract
Description
wherein BRIDGE is a substantially aliphatic, substantially neutral linker comprising from about 8 to about 150 non-hydrogen atoms; Q1 is a dye constituent selected from a fluorescent nucleic acid dye constituent, a non-fluorescent nucleic acid dye constituent, a fluorescent non-nucleic acid dye constituent, and a non-fluorescent non-nucleic acid dye constituent; Q2 is a dye constituent selected from a fluorescent nucleic acid dye constituent, a non-fluorescent nucleic acid dye constituent, a fluorescent non-nucleic acid dye constituent, and a non-fluorescent non-nucleic acid dye constituent. The dye constituents may be any of suitable dye constituents, such as those described herein, for example. Merely by way of example, the fluorescent nucleic acid dye constituent may be selected from an acridine dye, an asymmetric cyanine dye, a symmetric cyanine dye, a phenanthridinium dye, and a pyronin dye, and a styryl dye. At least one dye constituent of the Q1 dye constituent and the Q2 dye constituent is a reporter dye constituent, and at least one dye constituent of the Q1 dye constituent and the Q2 dye constituent is a fluorescent nucleic acid dye constituent or a non-fluorescent nucleic acid dye constituent. The reporter dye constituent and the fluorescent nucleic acid dye constituent may or may not be the same. The method may comprise performing a process using the test solution that would be sufficient for amplification of the target nucleic acid should the sample comprise the target nucleic acid. Merely by way of example, the process may be a PCR process, such as a real-time PCR process, for example. The method may comprise illuminating the test solution with light at a wavelength sufficient for absorption by the reporter dye constituent and determining fluorescent emission or a lack thereof.
wherein BRIDGE is a substantially aliphatic, substantially neutral linker comprising from about 15 to about 150 non-hydrogen atoms; Q1 is a dye constituent selected from a fluorescent nucleic acid dye constituent, a non-fluorescent nucleic acid dye constituent, a fluorescent non-nucleic acid dye constituent, and a non-fluorescent non-nucleic acid dye constituent; Q2 is a dye constituent selected from a fluorescent nucleic acid dye constituent, a non-fluorescent nucleic acid dye constituent, a fluorescent non-nucleic acid dye constituent, and a non-fluorescent non-nucleic acid dye constituent; Q3 is a dye constituent selected from a fluorescent nucleic acid dye constituent, a non-fluorescent nucleic acid dye constituent, a fluorescent non-nucleic acid dye constituent, and a non-fluorescent non-nucleic acid dye constituent. The dye constituents may be any suitable dye constituents, such as those described herein, for example. Merely by way of example, the fluorescent nucleic acid dye constituent may be selected from an acridine dye, an asymmetric cyanine dye, a symmetric cyanine dye, a phenanthridinium dye, and a pyronin dye, and a styryl dye. At least one dye constituent of the Q1 dye constituent, the Q2 dye constituent, and the Q3 dye constituent is a reporter dye constituent, and at least one dye constituent of the Q1 dye constituent, the Q2 dye constituent, and the Q3 dye constituent is a fluorescent nucleic acid dye constituent or a non-fluorescent nucleic acid dye constituent. The reporter dye constituent and the fluorescent nucleic acid dye constituent may or may not be the same. The method may comprise performing a process using the test solution that would be sufficient for amplification of the target nucleic acid should the sample comprise the target nucleic acid. Merely by way of example, the process may be a PCR process, such as a real-time PCR process, for example. The method may comprise illuminating the test solution with light at a wavelength sufficient for absorption by the reporter dye constituent and determining fluorescent emission or a lack thereof.
-L1-[A1-(CH2)α-]a[A2-(CH2)β-]b[A3-(CH2)γ-]c[A4-(CH2)δ-]d[A5- (CH2)ε-]e[A6-(CH2)ζ-]f[A7-(CH2)η-]g[A8-(CH2)θ-]h[A9-(CH2)τ-]i-A10-L2-
In this formula, each of L1 and L2, independently, is a moiety comprising a single bond; a polymethylene unit having 1 carbon to about 12 carbons, inclusive, optionally comprising at least one hetero atom selected from N, O and S; or an aryl optionally comprising at least one hetero atom selected from N, O and S; each of A1, A2, A3, A4, A5, A6, A7, A8, A9, and A10, independently, is a nucleic-acid-binding-enhancing-group (NABEG); a branched alkyl optionally comprising at least one hetero atom selected from N, O and S; or at least one saturated 5- or 6-membered ring, optionally comprising at least one hetero atom selected from N, O and S; each of α, β, γ, δ, ε, ζ, η, θ, and τ, independently, is zero or an integer from 1 to about 20, inclusive; and each of a, b, c, d, e, f, g, h, and i, independently, is zero or an integer from 1 to about 20, inclusive. BRIDGE may comprise a suitable number of non-hydrogen atoms, such as from about 8 to about 100 or about 150, inclusive, about 12 to about 60, inclusive, or about 15 to about 40, inclusive, merely by way of example. BRIDGE may comprise up to one positive charge, merely by way of example. BRIDGE may be any suitable linker molecule, such as any described herein, for example. In one example, BRIDGE has the formula:
—(CH2)x—C(═O)NH—(CH2)α—[O—(CH2)β]b—[O—(CH2)γ]c—NH(O═C)—(CH2)x—
wherein each x, independently, is an integer selected from 1 to 11, inclusive; α is an integer selected from 2 to about 20, inclusive; each of β□ and γ, independently, is 2 or 3; b is zero or an integer from 1 to about 20, inclusive; and c is zero or 1.
In the dye structures above, Ψ represents an anion, such as a iodide or a chlorine anion, merely by way of example.
In this formula, BRIDGE is a substantially aliphatic linker comprising from about 15 to about 150 non-hydrogen atoms and up to one positive charge; Q1 is a fluorescent nucleic acid dye constituent; Q2 is a fluorescent nucleic acid dye constituent; and Rr is a reactive group or a functional group. The reactive group or functional group may be any of suitable such groups, such as those described herein, for example. The composition may be any suitable composition, such as any of those described herein, for example. A method of using the composition, or dye, may comprise conjugating the composition to a substrate molecule, such as a substrate molecule selected from a nucleotide, an oligonucleotide, a peptide, a protein, a hapten, a drug, a microparticle, a synthetic polymer, a natural polymer, a biological cell, a virus, and a molecule of a solid surface.
In
-L1-[A1-(CH2)α-]a[A2-(CH2)β-]b[A3-(CH2)γ-]c[A4-(CH2)δ-]d[A5- (CH2)ε-]e[A6-(CH2)ζ-]f[A7-(CH2)η-]g[A8-(CH2)θ-]h[A9-(CH2)τ-]i-A10-L2-
—(CH2)α′-[A11-(CH2)β′-]a′[A12-(CH2)γ′-]b′[A13-(CH2)δ′-]c′A14
TABLE 1 |
Examples of Reactive Groups, Functional Groups, and |
Covalent Linkages |
Electrophilic Group | Nucleophilic Group | Resulting Covalent Linkage |
activated esters* | amines/anilines | Carboxamides |
acrylamides | Thiols | Thioethers |
acyl azides** | amines/anilines | Carboxamides |
acyl halides | amines/anilines | Carboxamides |
acyl halides | Alcohols/phenols | Esters |
acyl nitriles | Alcohols/phenols | Esters |
acyl nitriles | amines/anilines | Carboxamides |
aldehydes | amines/anilines | Imines |
aldehydes or ketones | Hydrazines | Hydrazones |
aldehydes or ketones | Hydroxylamines | Oximes |
alkyl halides | amines/anilines | alkyl amines |
alkyl halides | carboxylic acids | Esters |
alkyl halides | Thiols | Thioethers |
alkyl halides | alcohols/phenols | Esters |
alkyl sulfonates | Thiols | Thioethers |
alkyl sulfonates | carboxylic acids | Esters |
alkyl sulfonates | alcohols/phenols | Esters |
anhydrides | alcohols/phenols | Esters |
anhydrides | amines/anilines | Carboxamides |
aryl halides | Thiols | Thiophenols |
aryl halides | Amines | aryl amines |
aziridines | Thiols | Thioethers |
boronates | Glycols | boronate esters |
carboxylic acids | amines/anilines | Carboxamides |
carboxylic acids | Alcohols | Esters |
carboxylic acids | Hydrazines | Hydrazides |
carbodiimides | carboxylic acids | N-acylureas or anhydrides |
diazoalkanes | carboxylic acids | Esters |
epoxides | Thiols | Thioethers |
haloacetamides | Thiols | Thioethers |
halotriazines | amines/anilines | Aminotrizaines |
halotriazines | alcohols/phenols | triazinyl ethers |
imido esters | amines/anilines | Amidines |
isocyanates | amines/anilines | Ureas |
isocyanates | alcohols/phenols | Urethanes |
isothiocyanates | amines/anilines | Thioureas |
maleimides | Thiols | Thioethers |
phosphoramidites | Alcohols | phosphite esters |
silyl halides | Alcohols | silyl ethers |
sulfonate esters | amines/anilines | alkyl amines |
sulfonate esters | Thiols | Thioethers |
sulfonate esters | carboxylic acids | Esters |
sulfonate esters | Alcohols | Ethers |
sulfonyl halides | amines/anilines | Sulfonamides |
sulfonyl halides | phenols/alcohols | sulfonate esters |
*Activated esters, as understood in the art, generally have the formula □□COΩ, where Ω is a good leaving group, such as succinimidyloxy (□□OC4H4O2), sulfosuccinimidyloxy (□□OC4H3O2□□SO3H), or -l-oxybenzotriazolyl (□□OC6H4N3), for example; or an aryloxy group or aryloxy substituted one or more times by electron-withdrawing substituent(s), such as nitro, fluoro, chloro, cyano, trifluoromethyl, or combinations thereof, for example, used to form activated aryl esters; or a carboxylic acid activated by a carbodiimide to form an anhydride or mixed anhydride □□OCORa or □□OCNRaNHRb, where Ra and Rb, which may be the same or different, are independently C1-C6 alkyl, C1-C6 perfluoroalkyl, or C1-C6 alkoxy; or cyclohexyl, 3-dimethylaminopropyl, or N- morpholinoethyl. | ||
**Acyl azides can also rearrange to isocyanates. |
—(CH2)x—C(═O)NH—(CH2)α—[O—(CH2)β]b—[O—(CH2)γ]c—NH(O═C)—(CH2)x—
In one such case, for example, L1 of BRIDGE is —(CH2)x— and L2 of BRIDGE is —(CH2)x—, where each x, independently, is an integer selected from 1 to 11, inclusive; A1 of BRIDGE is —C(═O)NH—; a of BRIDGE is 1; A2 of BRIDGE is —O—; A3 of BRIDGE is —O—; α may be an integer selected from 2 to about 20, inclusive; each of β and γ, independently, may be 2 or 3; b may be zero or an integer selected from 2 to about 20; and c may be zero or 1; each of d, e, f, g, h and i of BRIDGE is 0; and A10 of BRIDGE is —NH(O═C)C—. Merely by way of example, BRIDGE may be as just described, wherein c is 1. Further, merely by way of example, BRIDGE may be as just described, wherein c is 1, and further, wherein x may be 5; α and γ may be the same and may be 2 or 3; β may be 2; and b may be 0, 1, 2 or 3.
Monomeric Dyes
TABLE 2 |
Prepared Fluorescent Nucleic Acid Dyes |
SPACER | ||||
LENGTH | ||||
No. | Name | Structure | MWt. | (ATOMS) |
1 | DMAO |
|
478.41 | N/ |
2 | TMAO |
|
620.35 | N/ |
3 | AO-3N |
|
705.16 | N/ |
4 | AO-2N |
|
493.43 | N/ |
5 | PMAO |
|
691.47 | N/ |
6 | AOAO-1 |
|
926.76 | 10 |
7 | AOAO-2 |
|
1124.03 | 21 |
8 | AOAO-3 |
|
1038.88 | 16 |
9 | AOAO-2Q |
|
1252.71 | 11 |
10 | AOAO-4 |
|
1041.95 | 14 |
11 | AOAO-5 |
|
896.73 | 8 |
12 | AOAO-6 |
|
1010.92 | 16 |
13 | AOAO-7 |
|
1080.96 | 19 |
14 | TOTO-3 |
|
1088.94 | 16 |
15 | AOAO-8 |
|
1064.92 | 16* |
16 | AOAO-9 |
|
1229 | 25 |
17 | AOAO-10 |
|
1313.24 | 31 |
18 | AOAO-11 |
|
1123 | 22 |
19 | AOAO-12 |
|
1082.94 | 19 |
20 | AOAO-13 |
|
1215.14 | 27 |
21 | AOAO-14 |
|
1621.61 | 53 |
22 | AOAO-12R |
|
1132.95 | 19 |
23 | AOTO-3 |
|
1094.99 | 16 |
24 | TOTO-12 |
|
1146.23 | 20 |
25 | TO(3)TO(3)- 12 |
|
1245.34 | 20 |
26 | TO(3)TO(3)- 2 |
|
1302.44 | 22 |
27 | AORO-7 |
|
1320.25 | 21 |
28 | RORO-12 |
|
1550.51 | 22 |
29 | TOTO-13 |
|
1248 | 27 |
30 | STST-27 |
|
1116 | 27 |
31 | STST-19 |
|
1000.8 | 19 |
32 | AOAO-47 |
|
1547.6 | 47 |
33 | AOAO-67 |
|
1864 | 67 |
33 | AOAO-113 |
|
2541 | 113 |
35 | ET-27 |
|
1239 | 27 |
36 | STST-21N |
|
1041 | 21 |
Claims (6)
-L1-[A1-(CH2)α-]a[A2-(CH2)β-]b[A3-(CH2)γ-]c[A4-(CH2)δ-]d[A5- (CH2)ε-]e[A6-(CH2)ζ-]f[A7-(CH2)η-]g[A8-(CH2)θ-]h[A9-(CH2)τ-]i-A10-L2-
—(CH2)α′-[A11-(CH2)β′-]a′[A12-(CH2)γ′]b′[A13-(CH2)δ′-]c′A14-,
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